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List of works by Mark Holder

A dirichlet process prior for estimating lineage-specific substitution rates

scientific article (publication date: March 2012)

A justification for reporting the majority-rule consensus tree in Bayesian phylogenetics

scientific article published in October 2008

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species

scientific article

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species

scholarly article published 18 October 2016

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species

An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy

scientific article

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics

scientific article

DendroPy: a Python library for phylogenetic computing

scientific article (publication date: 15 June 2010)

Difficulties in Detecting Hybridization

scientific article published on 01 November 2001

Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts.

scientific article published on 17 April 2011

Estimating trees from filtered data: identifiability of models for morphological phylogenetics

scientific article

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes

scientific article published in December 2008

Evidence for climate-driven diversification? A caution for interpreting ABC inferences of simultaneous historical events

scientific article

Explaining species distribution patterns through hierarchical modeling

article

Ginkgo: spatially-explicit simulator of complex phylogeographic histories

scientific article

Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics

scientific article published in December 2004

NeXML: rich, extensible, and verifiable representation of comparative data and metadata

scientific article (publication date: July 2012)

Phycas: software for Bayesian phylogenetic analysis

scientific article published on 9 January 2015

Phylesystem: a git-based data store for community curated phylogenetic estimates

article

Phylesystem: a git-based data store for community-curated phylogenetic estimates

scientific article

Phylogenetic assessment of filoviruses: how many lineages ofMarburg virus? ⬇️

scientific article published on July 1, 2012

Phylogeny estimation: traditional and Bayesian approaches

scientific article

Polytomies and Bayesian phylogenetic inference

scientific article published in April 2005

Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness

scientific article

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees

scientific article published in December 2011

Speeding up iterative applications of the Build supertree algorithm

The Posterior and the Prior in Bayesian Phylogenetics

scholarly article by Michael E. Alfaro & Mark Holder published December 2006 in Annual Review of Ecology, Evolution, and Systematics

The akaike information criterion will not choose the no common mechanism model

scientific article published on 31 May 2010

The big questions for biodiversity informatics

article

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The phylogenetic position of Myxozoa: exploring conflicting signals in phylogenomic and ribosomal data sets

scientific article

Two living species of coelacanths?

scientific article

What's in a likelihood? Simple models of protein evolution and the contribution of structurally viable reconstructions to the likelihood

scientific article

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